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H

Hong‐Bin Shen

Ministry of Education of China

71H-index
391Paper Count
1.9WCitation Count
Published Papers 116
Publication Date
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Structure-alignment-driven cross-graph modeling for functional RNA design
errNature Computational Science
IF18.3
err2026-07-30
err0
PREAI
errShengfan Wang; Jun Wang; Xiaojian Liu; Weimin Zhu; Jiaqi Huang; Yiming Xue; Junchi Yan; Hong-Bin Shen; Jie Song; Xiaoyong Pan
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errSave
SMENET: A Multi-View Semantic Model for Multi-Level Enzyme Function Prediction
errIEEE Transactions on Computational Biology and Bioinformatics
IF0
err2025-12-15
err0
PREAI
errHanwen Zhou; Wei Zhang; Zhaohong Deng; Guanjin Wang; Zhisheng Wei; Lei Wang; Xiaoyong Pan; Hong-Bin Shen; Dong-Jun Yu; Jing Wu
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errSave
Simultaneously infer cell pseudotime, velocity field, and gene interaction from multi-branch scRNA-seq data with scPN
errNAR GENOMICS AND BIOINFORMATICS
IF2.8
err2025-12-01
err0
PREAI
errZhou, Zhen; Li, Jiachen; Xin, Hongyi; Pan, Xiaoyong; Shen, Hong-Bin
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errSave
DMMAFS: Protein Function Prediction Based on Multi-Modal Multi-Attention Fusion Features
errIEEE Transactions on Computational Biology and Bioinformatics
IF0
err2025-11-01
err0
PREAI
errHe, Liangwen; Deng, Zhaohong; Hu, Fuping; Wang, Zhongyu; Zuo, Yun; Zhu, Lin; Chen, Haoran; Pan, Xiaoyong; Wei, Zhisheng; Wang, Lei; Shen, Hong-Bin; Yu, Dong-Jun; Wu, Jing
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errSave
A comprehensive proteome structural analysis suggests undiscovered functional domains in ocean archaea
errProtein Science
IF5.2
err2025-10-23
err0
PREAI
errYing Zhang; Yuan Liu; Peng Zhou; Xiaoyong Pan; James J. Chou; Hong-Bin Shen
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errSave
Modeling Enzyme Temperature Stability from Sequence Segment Perspective
errJournal of Chemical Information and Modeling
IF5.3
err2025-10-01
err0
PREAI
errZiqi Zhang; Shiheng Chen; Runze Yang; Zhisheng Wei; Wei Zhang; Lei Wang; Zhanzhi Liu; Fengshan Zhang; Jing Wu; Xiaoyong Pan; Hongbin Shen; Longbing Cao; Zhaohong Deng
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errSave
FoldExplorer: Fast and Accurate Protein Structure Search with Sequence-Enhanced Graph Embedding
errJournal of Molecular Biology
IF4.5
err2025-08-30
err0
PREAI
errYuan Liu; Ying Zhang; Zhen Zhou; Hong-Bin Shen
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errSave
Base-resolution binding profile prediction of proteins on RNAs with deep learning
errNUCLEIC ACIDS RESEARCH
IF13.1
err2025-08-12
err0
errOAAI
errLiu, Xiaojian; Zhu, Weimin; Ding, Xiaohan; Fang, Yi; Wang, Shengfan; Zhu, Lin; Shen, Hong-Bin; Pan, Xiaoyong
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errSave
Development of a multi-modal deep-learning-based web application for image classification of marine decapods in conservation practice
errFRONTIERS IN MARINE SCIENCE
IF3
err2025-05-12
err0
errOAAI
errZhou, Peng; Zhou, Zhinuo; Yang, Chenghan; Fang, Yi; Bu, Yu-Xin; Wang, Chun-Sheng; Zhang, Dong-Sheng; Shen, Hong-Bin
errShare
errSave
Identifying RNA-small Molecule Binding Sites Using Geometric Deep Learning with Language Models
errJOURNAL OF MOLECULAR BIOLOGY
IF4.5
err2025-04-01
err1
PREAI
errZhu, Weimin; Ding, Xiaohan; Shen, Hong-Bin
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errSave
RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning
errBMC BIOLOGY
IF4.5
err2025-03-11
err1
errOAAI
errPan, Xiaoyong; Fang, Yi; Liu, Xiaojian; Guo, Xiaoyu; Shen, Hong-Bin
errShare
errSave
A comprehensive survey on protein-ligand binding site prediction
errCURRENT OPINION IN STRUCTURAL BIOLOGY
IF7
err2024-06-01
err7
PREAI
errXia, Ying; Pan, Xiaoyong; Shen, Hong -Bin
errShare
errSave
Decoding protein binding landscape on circular RNAs with base-resolution transformer models
errCOMPUTERS IN BIOLOGY AND MEDICINE
IF6.3
err2024-03-01
err2
errOAAI
errWu, Hehe; Liu, Xiaojian; Fang, Yi; Yang, Yang; Huang, Yan; Pan, Xiaoyong; Shen, Hong-Bin
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errSave
DeepQs: Local quality assessment of cryo-EM density map by deep learning map-model fit score
errJOURNAL OF STRUCTURAL BIOLOGY
IF5.1
err2024-03-01
err4
PREAI
errFeng, Ming-Feng; Chen, Yu-Xuan; Shen, Hong-Bin
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errSave
TFvelo: gene regulation inspired RNA velocity estimation
errNATURE COMMUNICATIONS
IF15.7
err2024-02-15
err3
errOAAI
errLi, Jiachen; Pan, Xiaoyong; Yuan, Ye; Shen, Hong-Bin
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errSave
CRCS: An automatic image processing pipeline for hormone level analysis of Cushing's disease
errMETHODS
IF4.3
err2024-02-01
err2
PREAI
errLi, Haiyue; Xie, Jing; Song, Jialin; Jin, Cheng; Xin, Hongyi; Pan, Xiaoyong; Ke, Jing; Yuan, Ye; Shen, Hongbin; Ning, Guang
errShare
errSave
Multimodal variational contrastive learning for few-shot classification
errAPPLIED INTELLIGENCE
IF3.5
err2024-01-24
err2
PREAI
errPan, Meihong; Shen, Hongbin
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errSave
ZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions
errNATURE COMMUNICATIONS
IF15.7
err2023-11-29
err10
errOAAI
errWang, Yuxuan; Xia, Ying; Yan, Junchi; Yuan, Ye; Shen, Hong-Bin; Pan, Xiaoyong
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errSave
Understanding the mechanisms of halotolerance in members of Pontixanthobacter and Allopontixanthobacter by comparative genome analysis
errFRONTIERS IN MICROBIOLOGY
IF4.5
err2023-03-13
err0
errOAAI
errZhou, Peng; Bu, Yu-Xin; Xu, Lin; Xu, Xue-Wei; Shen, Hong-Bin
errShare
errSave
Cryo-EM image alignment: From pair-wise to joint with deep unsupervised difference learning
errJOURNAL OF STRUCTURAL BIOLOGY
IF5.1
err2023-03-01
err1
PREAI
errChen, Yu-Xuan; Feng, Dagan; Shen, Hong -Bin
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errSave

Research Directions

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Co-authors
Cooperation Journals
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Kuo‐Chen Chou
H-index: 124 · Papers: 483
周震 cover
周震 (Zhen Zhou)
H-index: 122 · Papers: 830
张洋 cover
张洋 (Yang Zhang)
H-index: 112 · Papers: 1.6K
K
Kuo‐Chen Chou
H-index: 92 · Papers: 239
J
Jian Yang
H-index: 91 · Papers: 1.0K
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